search for: chrx

...if df$exon appear several times: unique(df$exon) will show me the unique exons If I try to print only the unique exon lines with df[unique(df$exon),] -this doesn't print only the unique ones :( could you help? thanks Nat exon size chr start end 413077 ChrX_133594175_133594368_HPRT1 193 ChrX 133594175 133594368 413270 ChrX_133594183_133594368_HPRT1 185 ChrX 133594183 133594368 413455 ChrX_133594381_133594565_HPRT1 184 ChrX 133594381 133594565 413639 ChrX_133607389_133607495_HPRT1 106 ChrX 133607389 133607495 413745 ChrX_133607389_133607495_HPRT1...

Hello I am am new to R and any help with the following would be appreciated: I have a list (example attached) and I would like to create a new list which is a filtered version of this list. I.e I would like a list that only contains elements with this value: Chr 10 : 21853562 - 21855482 Any pointers/tips would be great. Thanks! Nikol -- Bioinformatician/Computer Associate Cambridge Institute

Hi R experts. how can I average two sets of columns? dd <- data.frame(b = c("chr2", "chr1", "chrY", "chr13", "chrX"),         w=11:15, x = 1:5, y = c(8, 3, 9, 9,7),        z = c(1, 1, 1, 2, 8)) expected result for mean(w,x) and mean(y,z) is 1  chr2 6  4.5 2  chr1 7  2 3  chrY 8  5 4 chr13 9  5.5 5  chrX 10 7.5 Yu [[alternative HTML version deleted]]

...the following powerpoint presentation? http://bmi.osu.edu/~khuang/IBGP705/BMI705-Lecture7.ppt (pages 36-37) In order to try to explain the graph, the way I see it in R terms is something like this: the "p-q" axis is a vector of positions (for example, seq(0,5000000,1)) the "Chr1-Chrx" is a vector of units, in this case chromosomes (so something like seq(1,10,1)) the plotted data is observations for each unit at each position I guess the fancy gradient on the highest peaks is tougher to get (knowing I am not an R expert), but just plain blue would suffice. I have checked...

...uot;chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chrX"), class = "factor"), start = c(5291000L, 10988025L, 11767950L, 11840900L, 12267450L, 12276675L), end = c(5291926L, 10988526L, 11768676L, 11841851L, 12268076L, 12277051L), peak = c(8L, 7L, 8L, 8L, 12L, 7L)), .Names = c("chrom", "start", "end", "peak...

...ying to make a fairly simple figure, but also trying to make it look "better" using ggplot2. I have data.frame that contains chrom length 1 chr1 249250621 2 chr2 243199373 3 chr3 198022430 4 chr4 191154276 5 chr5 180915260 6 chr6 171115067 7 chr7 159138663 8 chrX 155270560 9 chr8 146364022 10 chr9 141213431 11 chr10 135534747 12 chr11 135006516 13 chr12 133851895 14 chr13 115169878 15 chr14 107349540 16 chr15 102531392 17 chr16 90354753 18 chr17 81195210 19 chr18 78077248 20 chr20 63025520 21 chrY 59373566 22 chr19 59128983 23 chr22...

...hr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY") #access/group the by subset of annotation annotGr <- exons(txdb) #annotGr <- cds(txdb) wholeGenomeMatch <- function() { for(i in chrList) { #matches on plus strand matches.plus.strand <- matchPattern(query.plus, Hsapiens[[i]], fixed=FALSE, max....